Zimmerman needs to add more "bedside manner" to his original EMH in order to make this new hologram as realistic as possible, so he conducts a series of extensive interviews with everyone who knows Bashir. It becomes apparent that Doctor Zimmerman is very thorough, so Bashir asks, as a personal favor, that Zimmerman not interview Bashir's parents as the three are estranged from each other. Zimmerman says he understands, but rather than honoring his request, he is just far more eager to get in touch.

Zimmerman has Dr. Bashir's parents, Richard and Amsha, brought to Deep Space 9, much to Bashir's obvious chagrin. Bashir is not pleased to see them and expresses his displeasure to Dr. Zimmerman, who responds that a complete profile is necessary. The Bashirs have fallen out over a secret about Julian's past and over-expectant pressure that they placed upon him during his youth.

Richard Bashir has a long history of starts and stops, constantly changing jobs, never completing a project. His current occupation is designing public parks on Earth. Julian is scornful of his father's consistent lack of focus or satisfaction, and his unwillingness to take responsibility for his actions. The elder Bashirs defend themselves, saying they did the best they could. Julian leaves the room, dissatisfied.

Remorseful, Richard goes to the holographic lab to apologize. Richard pledges to Julian, standing in befuddled silence, that he will never reveal Julian's genetically engineered past, that he is proud of what Julian has become. Unfortunately, it turns out that Richard has unknowingly apologized to the Long-term Medical Holographic program. Richard inadvertently gave away their dark secret to Chief O'Brien and Zimmerman, who were in the back room. O'Brien then has to tell Julian that Zimmerman will be reporting that he is unsuitable as the LMH model due to his "suspected" genetic engineered background. The report will be filed with Starfleet Medical, and this would eventually lead to Julian's dismissal from Starfleet and his license to practice medicine being revoked.

Dr. Bashir confronts his parents after this incident. It is revealed that when Julian was young, he had some form of learning disability or possible mental disability. His parents perceived his gross deficits as defects. So, they went outside of the Federation (and its laws) to have their child genetically engineered on Adigeon Prime so that he would be able to keep up with his peers. Bashir ended up not only as bright as his classmates, but brighter, fitter, stronger and faster as well, thus beginning his second life. But now that second life would end, because of strict Federation laws banning genetic engineering for anything except for repairing serious birth defects.

Dr. Bashir decides that resigning his commission would prevent an inquiry, thus protecting his family and himself from serious repercussions. However when he enters Captain Sisko's office, his father is already there, having told the Captain everything and taking full responsibility for the situation. Bashir's father agrees to go to prison for two years so that Bashir can keep his medical license and his position within Starfleet aboard Deep Space 9.

Meanwhile, Rom tries to work up his courage to ask Leeta, one of Quark's dabo girls, out, but he chickens out when she approached him. Quark reminded him of the time he signed a five-year contract with Prinadora so he could have Nog. But he fell so deeply in love with her that he tried to extend the contract. However, he failed to read the fine print – Prinadora's father swindled him out of all his money and she left him for a richer Ferengi, leaving him with Nog.

Julian introduced Leeta to Zimmerman who he immediately takes a liking to. He promises Leeta her own store at the Jupiter Station. But before they can leave, Rom comes in screaming to confess his love of Leeta. She reciprocates and they start kissing. Zimmerman, seeing that true love has made him obsolete, leaves, following another rather gorgeous alien.

"He needs a woman with body and brains".
"I have brains."
"Sure you do, honey. That's why I hired you. Now eat up and then take those brains back to the dabo wheel where the customers can get a good long look at them."

- Quark and Leeta

"She's a female, Rom, and the one constant in the universe is: females are trouble."

- Quark, to Rom (about his former wife Prinadora)

"Why is everyone so worried about holograms taking over the universe?"

- Lewis Zimmerman

"Note, contact subject's parents immediately."

- Lewis Zimmerman, just after Bashir asks him to not contact his parents

"Wow, think of it, Julian. If this thing works you will be able to irritate hundreds of people you never even met."

"What do you want me to do?"
"Just stand there and look like a doctor... if you can."

- Bashir and Lewis Zimmerman, when Zimmerman is about to download the optical parameters for the program

"Beginning data transferral."
"Data transferral?! Am I being replaced?"
"You're being supplemented by a new long term program."
"By him!?"
"There, transfer complete."
"Please state the nature of the medical emergency."
"Oh, that's original! He doesn't even look old enough to be a doctor!"
"If you want my advice, you should delete this program. Now that I'm here, why would you want an archaic piece of software like him?"
"Archaic!?"
"We can discuss this at another time."

- Lewis Zimmerman, EMH, and Long-term Medical Holographic program.

"Waaaiiit..."

- Rom, about not wanting Leeta to leave the station.

"I'm still your father, Jules and I will not have you talk to me like that."
"No. You used to be my father. Now you're my architect, a man who designed a better son, to replace the defective one he was given. Well, your design has a built-in flaw. It's illegal."

"You decided I was a failure in the first grade."
"Jules, you don't understand. You never did... "
"No, you don't understand! I stopped calling myself Jules when I was fifteen and I'd found out what you'd done to me! I'm Julian!"
"What difference does that make?"
"It's makes every difference! Because I'm different, can't you see? Jules Bashir died in that hospital, because you couldn't live with the shame of having a son who didn't measure up!"

- Julian and Richard Bashir

"You've never had a child. You don't know what it's like to watch your son... to watch him fall a little further behind every day. You know he's trying, but something's holding him back. You don't know what it's like to stay up every night worrying that maybe it's your fault; maybe you did something wrong during the pregnancy, and maybe you weren't careful enough. Or maybe there's something wrong with you; maybe you passed on a genetic defect without even knowing it."
"Amsha..."
"No, this is important. You can condemn us for what we did; you can say it's illegal or immoral or whatever you want to say. But you have to understand that we didn't do it because we were ashamed. But because you were our son. And we loved you."

- Amsha and Richard Bashir explaining to Julian why they had him genetically enhanced

"Two hundred years ago, we tried to improve the species through DNA resequencing. And what did we get for our troubles? The Eugenics Wars. For every Julian Bashir that can be created, there's a Khan Singh waiting in the wings — a superhuman whose ambition and thirst for power have been enhanced along with his intellect. The law against genetic engineering provided a firewall against such men. And it's my job to keep that firewall intact."

In Jimmy Diggs' original version of this story, the Bashir/Zimmerman plot was the B-story. The producers were uninterested in the A-story, but they loved the idea of Zimmerman using Bashir as the model for the LMH and decided that it was worthy of being an A-story in and of itself. However, they were aware that a comedy show dealing with holographic doctors would not be enough to sustain an entire episode, and they decided that to make things more interesting, Zimmerman would have to discover some dark secret from Bashir's past. As René Echevarria says of Ronald D. Moore, "his instinct was that there needed to be some big secret that Zimmerman uncovers, but we couldn't, for the life of us, think what it would be." According to Moore, "I kept saying 'What's the secret of Bashir's past? What's the thing that this guy Zimmerman is going to find that's so interesting?' I remember that René and I started talking about genetics, and René pointed out that genetic engineering is one of the things that is oddly missing in the Star Trek universe. It's a concept that's very much out there in science fiction, and even in the real world of science, but in Star Trek, it's virtually never discussed, aside from the fact that there was this thing called the Eugenics Wars at some point, and Khan came out of it." That conversation ultimately led Moore to come up with the idea that Bashir was genetically altered. (Star Trek: Deep Space Nine Companion)

In explaining any potential continuity problems between the revelation that Bashir is genetically enhanced and the previously established behavior and personality of the character, Ronald D. Moore explained, "It really explained a lot about the character to me. He'd had some strange jigs and jags in his profile over the course of the first four seasons. We have this guy with a lot of arrogance, who almost became a tennis player, who has all these different tales of why and when he went to medical school, and why he didn't become valedictorian of his class, and who has something about his past on Earth that he doesn't want to talk about. When Odo was going to Earth in "Homefront", he asked Bashir 'Is there anybody you want me to look up?' and Bashir says 'I have nobody there I want to talk to.' There was something in this guy's back-story that was interesting, And it suddenly all made sense if this was a guy who'd been genetically engineered to be very, very smart but who'd had to hide it all his life." (Star Trek: Deep Space Nine Companion)

Originally, this episode ended very differently to its finished form. In the original story, O'Brien finds out that there are problems with the LMH which have been caused deliberately by Zimmerman because he doesn't want it to replace the EMH. Bashir then informs O'Brien that Zimmerman is planning to reveal his genetic engineering secret, so O'Brien goes to see Zimmerman and tells him that if he exposes Bashir, his deliberate errors with the LMH will also be exposed. As such, there is a trade-off, and neither secret is revealed. The reason this story was altered was actually Alexander Siddig. He didn't want to play the character as having a secret that only he, O'Brien and the audience knew about. He thought the long-term implications of this on his performance could be detrimental, having to portray the character every week as being in possession of this secret, and allowing it to inform everything he does, but in such a way that none of the other characters notice anything unusual. As such, Siddig managed to convince the writers to alter the end of the story so that the truth is revealed to all. (Star Trek: Deep Space Nine Companion)

When Admiral Bennett reminds Bashir of the risks of genetic engineering by referencing the Eugenics Wars, he referred to it as having occurred "two hundred years ago." However, established continuity suggests that he is about 200 years off. Ronald D. Moore comments: "This is my personal screw-up. When I was writing that speech, I was thinking about Khan and somehow his dialog from "Wrath" started floating through my brain: "On Earth... 200 years ago... I was a Prince..." The number 200 just stuck in my head and I put it in the script without making the necessary adjustment for the fact that "Wrath" took place almost a hundred years prior to "Dr. Bashir." I wrote it, I get the blame." (AOL chat,1997) Of course, one explanation is that Admiral Bennett himself got the date wrong. According to Joe Menosky, rumor originally suggested that the discrepancy would be less excusable. Menosky remembered, "I heard they were going to point blank, have a statement that said the Eugenics Wars occurred in the 21st century. That was the rumor that was floating through the building. I think that people would have hit the roof if they would have done that, so maybe they just decided to leave it up in nebulous hyperspace. The point is, if they would have gone that route, then you would have had to come up with some theory about how history got screwed up. The records got destroyed, or something messed up the original dates." (Cinefantastique, Vol. 29, No. 6/7, p. 110)

After Jimmy Diggs pitched the story for this episode, he didn't hear back from the producers for over a year. When he eventually did get a call from Ronald D. Moore, he thought it was a friend playing a practical joke on him, and he made Moore prove he was who he said he was. (Star Trek: Deep Space Nine Companion)

Ira Steven Behr commented: ""Doctor Bashir I Presume" was a terrific episode, but I was never totally comfortable with Julian's genetic engineering. It was one of those revelations that did not seem quite authentic to me. We'd had to work backward to get it. So I felt we needed to do something to help the idea along". Behr's thoughts would lead to the development of "Statistical Probabilities". (Star Trek: Deep Space Nine Companion)

Alexander Siddig commented: "I think 'Doctor Bashir, I Presume' was probably the best one I got to do. It was a really good idea for an episode, and it had some interesting elements in it. Bob Picardo was great. The guy is a blast, a lot of fun. I'd known him before doing the show, but only on an acquaintance level. We'd met at a convention in Australia and in a couple of other places. He's really good. He can come back again if he wants to - I'd hire him! I also liked in that episode they finally gave Bashir parents, because we hardly knew anything about his family before then. And on top of that they have me parents who'd given me a tricky life. The whole genetic engineering issue, I thought, was an interesting double whammy. I went from getting Bashir ready to become this wonderful holographic doctor to realizing that he was actually a fraud. That's really good stuff". ("A Truly Model Doctor", Star Trek Monthly issue 30)

Siddig was not pleased the way he was informed of the revelation about Bashir in the episode. "I didn't know about it on Tuesday, and on Thursday the script arrived – we started shooting on Friday. I was so shocked. You know you get the impression that maybe the producers sit down and talk about strategies and character arcs with actors but this thing came out of the blue and pissed me off so royally." ([1])

Ronald D. Moore commented: "I had a lot of fun with 'Doctor Bashir I Presume'. I thought that was an interesting show in that it suddenly takes a left turn. Just when you think it's a farce and is going to be all about the EMH program and his parents and people running about being silly, it's like 'Whoa! What's this? There's character revelations here'. So I like that". ("Writing Across the Universe", Star Trek Monthly, issue 29)

Robert Picardo commented: "The little appearance on Deep Space Nine was great fun. You know, we're all acquainted with each other from working on the same lot, and from making public appearances together, but we don't often have the opportunity to work together, so that was nice. I had a good time with Sid and Colm Meaney". Picardo commented that he would have liked to have appeared in the series again. ("Doctor at Large", Star Trek Monthly issue 30)

Brian George commented "I'm a journeyman. I go from job to job. Most times, you're just a fifth wheel and the producers are only concerned about the stars. It was wonderful to get a role that required some acting, that actually required some thought and preparation, and then to get a director who considered me as important as the regulars". ("Parenthood", Star Trek Monthly, issue 36)

This episode is the first to provide any details whatsoever about Nog's mother, Prinadora. Indeed, it is the only episode to do so. She would be mentioned again in "Ferengi Love Songs", but no new information would be presented.

Dr. Lewis Zimmerman was named for Herman Zimmerman, a production designer for TNG, DS9, and the four TNG movies.

The title of this episode is in reference to the famous quote "Doctor Livingstone, I presume?" spoken by Henry Morton Stanley in 1869. Stanley was a reporter sent by the New York Herald to find Dr. David Livingstone in Africa. Livingstone was a missionary and explorer who had lost contact with the outside world for six years. When Stanley found Livingstone, he greeted him with those now famous words. Coincidentally, this episode was directed by David Livingston.